Anime Recommendation and Suggestion Query

[Ryllharu]

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Damn, I took too long, but I completely second Alien Nine, and Now and Then, Here and There from Pandadice. I haven't seen the other two (but I have heard of them).
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Putting the more mainstream titles aside for a second:

Real Drive (RD Sennou Chousashitsu) - Cyberpunk dealing with the environment, nanotech, virtual reality, androids, cyborgs, and a healthy dose of metaphysics. It's a bit more toward present day tech than Ghost in the Shell, and it is also written by Masamune Shirow. It's very much the sci-fi extension of a constantly-connected society. Moreover, there is an interesting catch of the main heroine not having a cyberbrain, where nearly all her peers do. The episodes are a nice mix of stand alone, exploratory or comedy relief episodes and intermingled well with the overarching plot episodes. Perfect coming off Dennou Coil, because they both have similar themes and a detective series framework.
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Planetes - Space garbage collectors. While this isn't nearly as obscure as Real Drive became, as a somewhat older series, it may not always get the attention it earned. This is one of the best near-future space series I've watched. Slice of life most of the time, it has a very realistic view of space development and exploration, as well as a great awareness of all the very real hazards for humanity. Any anime sci-fi fan would consider this one of the masterpieces of the genre.
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ARIA - Yes, I am throwing in ARIA here. You will either love or hate this series, unequivocally. What makes ARIA special is that while on the surface it is simply a slice of life series about girls piloting tour gondolas, there is a lot of sci-fi undertones that often go unnoticed, even by fans of the series. There is a great deal of technology and history behind the terraforming of the planet once known as Mars into a water paradise. The series also has a rather informative idealized version of Venice. It is worth the try.
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Starship Operators - This is another one of my favorite space anime series. This series perhaps features the highest level of actual and realistic strategy in anime that I've had the pleasure of watching. Battles operate like 19th Century Naval battles. They can take days of maneuvering, but often end in a single shot. Strategy both martial and political take absolute precedence here in a battle of graduating trainees fighting a war of liberation, by funding their war through exclusive television coverage and political under the table deals.
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Returning to the more mainstream or better known titles:

Crest of the Stars / Banner of the Stars - Largely considered one of the "masterpieces" of anime. It is a political epic in space. I haven't finished it myself, so I can't elaborate as well as I should.
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Ghost in the Shell : Stand Alone Complex - I prefer the universe of the series to the films myself, but if you haven't seen both of the two GiTS universes, you really should. They are one of the pillars of sci-fi anime as well as cyberpunk in general. The series just gives you more of it, expands on the side characters, and has an excellent mix of action episodes, detective episodes, and less serious episodes.

Ergo Proxy - You've probably already heard of this one. Weird and sci-fi sure fit the bill here.
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RahXephon - Like a really weird, music-centric Evangelion.
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Kurau Phantom Memory - Sci-fi in general and superpowers founded in sci-fi science.
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Hyper Police - I might not call it a "masterful" series, but it is very enjoyable. A detective/bounty hunter series taking place on a somewhat post-apocalyptic world where humans are endangered and monsters and beastmen intermingle with them. It is a fun series worth giving a try. Certainly one that has a retro feel by today's standards, but it was 1997.
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Mahoromatic - The most prominent combat android turned maid series. Fun, but with plenty of depressing undertones at the conclusion of each episode. You may have missed it in your viewings, and it is certainly one you would want to check out.
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I think that about does it, but Real Drive is probably your best bet.